Lexi Walls is a third-year biochemistry graduate student in David Veesler’s Structural Biology lab. For her, HPC is a means to study coronaviruses, such as SARS (severe acute respiratory syndrome) and MERS (Middle Eastern respiratory syndrome). SARS was first detected in 2002, when over 8,000 people were infected and the virus had a 10% fatality rate. MERS infections began in 2012 and are still ongoing with a 35% fatality rate. Walls is hoping to exploit the structure of proteins behind these diseases in order to design better vaccines against them.
Cryo-electron microscopy is used to discover, or “resolve”, protein structure. This procedure is a neat tool for imaging proteins that are reluctant to crystallize. It is done by freezing a batch of proteins in liquid ethane and then imaging the non-crystalline ice. Specifically, Walls collects about 1500 micrograph images of the frozen, tumbling proteins in 48 hours. Cryo-EM uniquely enables looking at biological macromolecules in a near-native state, since they are frozen in the shapes that they take on in everyday life.
With these images in tow, Walls can then use highly parallelized algorithms to solve for the proteins’ atomic resolution structures – ultimately a list of amino acid coordinates in three dimensions. The algorithms align, unblur, and average the 2D images of the proteins, and the more images there are of proteins at slightly different tilts and conformations, the more precise the 2D class averages will show the various orientations. The more precise these 2D classes are, the higher the resolution of the final 3D protein reconstruction. The software used to take particle images all the way to a 3D map is called Relion. This map is then used to build atomic models of the amino acid coordinates using RosettaCM, de novo, and beam search softwares in collaboration with another HPC student Brandon Frenz in the Dimaio laboratory.
The software packages that Walls uses are getting increasingly streamlined to facilitate biochemists in a user-friendly way. One and a half years ago, she had never programmed nor connected to a supercomputer terminal. But in just a few focused months, she was able to feel comfortable with basic Linux and the software packages that her lab runs on HYAK. This transformation should bring comfort to all HPC-newbies! Walls wonders why so few undergrads are present in the labs around her.
Walls’ next step will be to start using the protein structures that she is uncovering to aid real vaccine design. For instance, she can investigate how her new knowledge accounts for the successes of previous vaccines, and how she can dive into previously unnoticed interacting regions. She can also see which areas of the virus proteins are most conserved in sequence and structure, and try to exploit them as antigens.
The explosion in Cryo-EM automation, precision, and supercomputer availability over the last couple years is making this technique a novel gold standard for protein model-building in the bioengineering world. It’s letting Walls work in an incredible intersection of fields, and she is excited to see more and more research groups begin to use it.